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--- processing:complex-multi-phase [2023/12/10 09:32] – smerkel
+++ processing:complex-multi-phase [2023/12/10 12:11] (current) – smerkel
@@ Line 20: / Line 20: @@
 To do so, it is much better to work on an [[processing:phase_identification| 2θ-histogram of the experimental g-vectors]].
-The figure on the left shows an example from Gay //et al// //Earth and Planetary Science Letters// 604 (2023) [doi: [[https://doi.org/10.1016/j.epsl.2023.118015| 10.1016/j.epsl.2023.118015]]]. The sample holds 4 sample phases and a pressure medium (KCl). Top image is an ω-stack for all experimental g-vectors, potted as a function of ds and η. The bottom image is what you get if you try to index an average diffraction image directly. The middle panel is what is extracted from a 2θ-histogram of the experimental g-vectors.
+The figure on the right shows an example from Gay //et al//, published in //Earth and Planetary Science Letters// in 2023 [doi: [[https://doi.org/10.1016/j.epsl.2023.118015| 10.1016/j.epsl.2023.118015]]]. The sample holds 4 sample phases and a pressure medium (KCl). Top image is an ω-stack for all experimental g-vectors, potted as a function of ds and η. The bottom image is what you get if you try to index an average diffraction image directly. The middle panel is what is extracted from a 2θ-histogram of the experimental g-vectors.
-The histogram is less affected by very large grains (the pressure medium in our case). In addition, experimental peak broadening, due to the experiment or the sample properties such as grain size or microstrains, have been removed since we only consider the center of mass of eack peak.
+The histogram is less affected by very large grains (the pressure medium in our case). In addition, experimental peak broadening, due to the instrument or the sample properties such as grain size or microstrains, have been removed since we only consider the center of mass of eack peak.
 You can then use your favorite powder diffraction software, such as [[https://github.com/seto77/PDIndexer|PDIndexer]] or [[https://luttero.github.io/maud/ | MAUD]] to identify sample phases and their unit cell parameters. Just keep in mind that peak intensities in the histograms are not true intensities, but a number of experimental g-vectors.
@@ Line 37: / Line 37: @@
 In our case, we do not index peaks from the pressure medium, but simply ignore the corresponding 2θ in the indexing. This can be easily done by specifying custom 2θ ranges in the GrainSpotter input file.
-===== Idedexing loop =====
+===== Indexing loop =====
 Let's say your sample consist of 3 phases, phaseA, phaseB, phaseC, with the 3 corresponding experimental GVE files, phaseA.gve, phaseB.gve, phaseC.gve. The indexing process will go as follows
@@ Line 46: / Line 46: @@
   * index grains for phaseC, with a strict set of tolerances,
   * remove the assigned experimental g-vectors from all 3 phaseA.gve, phaseB.gve, and phaseC.gve,
-  * and repeat the process as many times as necessary, with the same tolerances, and then increasing tolerances to catch most sample grains.
+  * and repeat the process as many times as necessary, with the same tolerances, and then increasing tolerances to catch most sample grains, merging all the indexed grains into one master file.
+You can either run this by hand, your use a fancy loop with a bash script. We actually spent some time working on such a loop, and you can find an [[examples:gs_loop_multiphase|example of a multiphase indexing loop here]].
+===== Preparing figures =====
+This will be written later. We are still waiting for some publications to be accepted.